data_6IKZ # _model_server_result.job_id vIciNXugCx_tS6t3ftC1ug _model_server_result.datetime_utc '2025-07-07 03:15:29' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 6ikz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":301}' # _entry.id 6IKZ # _exptl.entry_id 6IKZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 484.141 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE 5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 6IKZ _cell.length_a 119.025 _cell.length_b 119.025 _cell.length_c 108.244 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6IKZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 8_554 -y,-x,-z-1/2 0 -1 0 -1 0 0 0 0 -1 0 0 -54.122 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id I _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C9 H15 N2 O15 P3' _chem_comp.formula_weight 484.141 _chem_comp.id UTP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE 5'-TRIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag PA O1A UTP doub 359 n n PA O2A UTP sing 360 n n PA O3A UTP sing 361 n n PA O5' UTP sing 362 n n O2A H2A UTP sing 363 n n O3A PB UTP sing 364 n n O5' C5' UTP sing 365 n n PB O1B UTP sing 366 n n PB O2B UTP doub 367 n n PB O3B UTP sing 368 n n O1B H1B UTP sing 369 n n O3B PG UTP sing 370 n n PG O1G UTP sing 371 n n PG O2G UTP doub 372 n n PG O3G UTP sing 373 n n O1G H1G UTP sing 374 n n O3G H3G UTP sing 375 n n C5' C4' UTP sing 376 n n C5' "H5'1" UTP sing 377 n n C5' "H5'2" UTP sing 378 n n C4' O4' UTP sing 379 n n C4' C3' UTP sing 380 n n C4' H4' UTP sing 381 n n O4' C1' UTP sing 382 n n C1' C2' UTP sing 383 n n C1' N1 UTP sing 384 n n C1' H1' UTP sing 385 n n C2' O2' UTP sing 386 n n C2' C3' UTP sing 387 n n C2' H2' UTP sing 388 n n O2' HA UTP sing 389 n n C3' O3' UTP sing 390 n n C3' H3' UTP sing 391 n n O3' HB UTP sing 392 n n N1 C6 UTP sing 393 n y N1 C2 UTP sing 394 n y C6 C5 UTP doub 395 n y C6 H6 UTP sing 396 n n C2 O2 UTP doub 397 n n C2 N3 UTP sing 398 n y N3 C4 UTP sing 399 n y N3 H3 UTP sing 400 n n C4 O4 UTP doub 401 n n C4 C5 UTP sing 402 n y C5 H5 UTP sing 403 n n # _atom_sites.entry_id 6IKZ _atom_sites.fract_transf_matrix[1][1] 0.008402 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008402 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.009238 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 SO4 A 1 301 2 SO4 SO4 . D 2 SO4 A 1 302 3 SO4 SO4 . E 2 SO4 A 1 303 4 SO4 SO4 . F 2 SO4 A 1 304 5 SO4 SO4 . G 3 PPV A 1 305 1 PPV PPV . H 4 GOL A 1 306 1 GOL GOL . I 5 UTP B 1 301 2 UTP UTP . J 2 SO4 B 1 302 1 SO4 SO4 . K 2 SO4 B 1 303 6 SO4 SO4 . L 6 HOH A 1 401 13 HOH HOH . L 6 HOH A 2 402 3 HOH HOH . L 6 HOH A 3 403 14 HOH HOH . L 6 HOH A 4 404 11 HOH HOH . M 6 HOH B 1 401 5 HOH HOH . M 6 HOH B 2 402 12 HOH HOH . M 6 HOH B 3 403 4 HOH HOH . M 6 HOH B 4 404 15 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P PA UTP . . . I 5 12.694 13.344 -34.171 1 180.38 ? PA UTP 301 B 1 HETATM 2 O O1A UTP . . . I 5 12.344 13.922 -35.504 1 175.26 ? O1A UTP 301 B 1 HETATM 3 O O2A UTP . . . I 5 12.973 11.882 -34.137 1 178.36 ? O2A UTP 301 B 1 HETATM 4 O O3A UTP . . . I 5 13.962 14.126 -33.561 1 174.45 ? O3A UTP 301 B 1 HETATM 5 O O5' UTP . . . I 5 11.553 13.722 -33.094 1 168.98 ? O5' UTP 301 B 1 HETATM 6 P PB UTP . . . I 5 15.511 13.833 -33.256 1 163.89 ? PB UTP 301 B 1 HETATM 7 O O1B UTP . . . I 5 15.94 14.7 -32.121 1 145.14 ? O1B UTP 301 B 1 HETATM 8 O O2B UTP . . . I 5 15.753 12.364 -33.185 1 172.07 ? O2B UTP 301 B 1 HETATM 9 O O3B UTP . . . I 5 16.196 14.382 -34.596 1 168.9 ? O3B UTP 301 B 1 HETATM 10 P PG UTP . . . I 5 16.067 13.965 -36.154 1 173.71 ? PG UTP 301 B 1 HETATM 11 O O1G UTP . . . I 5 15.285 12.666 -36.168 1 168.69 ? O1G UTP 301 B 1 HETATM 12 O O2G UTP . . . I 5 15.331 15.091 -36.834 1 171.52 ? O2G UTP 301 B 1 HETATM 13 O O3G UTP . . . I 5 17.486 13.812 -36.66 1 157.67 ? O3G UTP 301 B 1 HETATM 14 C C5' UTP . . . I 5 10.531 14.695 -33.471 1 158.32 ? C5' UTP 301 B 1 HETATM 15 C C4' UTP . . . I 5 9.823 15.267 -32.259 1 147.11 ? C4' UTP 301 B 1 HETATM 16 O O4' UTP . . . I 5 8.542 15.843 -32.639 1 132.19 ? O4' UTP 301 B 1 HETATM 17 C C1' UTP . . . I 5 7.557 14.828 -32.596 1 114.84 ? C1' UTP 301 B 1 HETATM 18 C C2' UTP . . . I 5 8.186 13.634 -31.855 1 126.4 ? C2' UTP 301 B 1 HETATM 19 O O2' UTP . . . I 5 7.36 13.021 -30.888 1 127.33 ? O2' UTP 301 B 1 HETATM 20 C C3' UTP . . . I 5 9.406 14.27 -31.176 1 139.05 ? C3' UTP 301 B 1 HETATM 21 O O3' UTP . . . I 5 9.096 14.915 -29.945 1 140.82 ? O3' UTP 301 B 1 HETATM 22 N N1 UTP . . . I 5 7.173 14.472 -33.986 1 97.76 ? N1 UTP 301 B 1 HETATM 23 C C6 UTP . . . I 5 7.798 15.03 -35.083 1 103.54 ? C6 UTP 301 B 1 HETATM 24 C C2 UTP . . . I 5 6.209 13.491 -34.155 1 100.01 ? C2 UTP 301 B 1 HETATM 25 O O2 UTP . . . I 5 5.631 12.942 -33.227 1 97.75 ? O2 UTP 301 B 1 HETATM 26 N N3 UTP . . . I 5 5.935 13.159 -35.46 1 104.72 ? N3 UTP 301 B 1 HETATM 27 C C4 UTP . . . I 5 6.514 13.678 -36.602 1 105.02 ? C4 UTP 301 B 1 HETATM 28 O O4 UTP . . . I 5 6.156 13.259 -37.707 1 91.54 ? O4 UTP 301 B 1 HETATM 29 C C5 UTP . . . I 5 7.506 14.684 -36.35 1 102.35 ? C5 UTP 301 B 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 29 #